Hi guys my name is Nick Dulock and I am a rising senior at Regis High School in New York City. Outside of school, I run cross country, fence, and tutor a lot (primarily at an organization called BTNY). In school, I participate in a myriad of clubs (perhaps a few many), and run Indian Cultural Society, Pop Culture Club, and Science Journal.
As far as science goes, I'm kind of all over the place. I've studied and researched subjects all the way from hydrogeology to alternate energy to biodiversity/conservation genetics. The common factor here has been a strong interest in environmental sciences and the application of such for a cleaner and more earth-friendly future.
Design Presentation: Bioremediation of Subsidence through Microbial Induced Calcite Precipitation
What is Subsidence? Simply defined, land subsidence is the lowering of the ground level. To clarify, subsidence does not involve sinkholes, which occur due to the dissolution of soluble bedrock by water in a respectively small area. Rather, subsidence is a result of a lack of water within an aquifer that generally affects a large area, and therefore is often unable to be observed without prior cognition of the issue or access to machines called extensometers.
By natural processes, this can be the outcome of tectonic activities or the compression of land and withdrawal of water by the generation of ice sheets over the Earth’s crust. While the natural procession of subsidence does present a threat to current land possessions and man-made establishments, the true concern is artificially-induced subsidence precipitated from human activities. Human-induced land subsidence has not only catalyzed natural subsidence but has rapidly stimulated lowering in areas otherwise indisposed to such dramatic geologic change. Primarily, land subsidence is induced by oil and gas drilling which interferes with an aquifer’s structural integrity, and more significantly, the excessive drainage of water from aquifer’s. This last method which quite literally drains it of essential support. Drainage-induced subsidence can ultimately be illustrated as the following. Recall the water table— the area beneath the earth in which lies [water] saturated bedrock. This saturated bedrock is called an aquifer, through which ground water filters and flows. The groundwater within non-polluted aquifers is not only essential for fulfilling nutritional requirements, but also for irrigation, farming, and manufacturing processes, and therefore aquifers are tapped into through wells and the likes. However, the overexertion of these wells and strained drainage in order to fulfill these needs often results in an insufficient quantity of water remaining in the aquifer; not only that, but it also undermines its ability to recuperate the water it has lost.
Because the water within aquifers is actually essential to holding up the ground, by withdrawing it without permitting it to sufficiently recover, the ground literally “caves” in on itself. The bedrock particles compact together, closing drainage and underground water systems and therefore prohibiting flow as well as restricting storage capacity. This is the most prominent form of subsidence, and currently it presents a strong yet often-overlooked and unidentified danger to our world.
Observable Effects --From here on, when I refer to subsidence I will be referring to human-induced subsidence, primarily as a result of excessive aquifer-drainage--
Subsidence is still a developing issue, as the public lacks much awareness of its existence, processes, effects, and hazard. That being said, it is a persistent and unavoidable occurrence that will persevere as long as our current needs and methodology do not consider the effects they precipitate. Presently, subsidence is rampant not only in the United States, but also Thailand, Japan, Italy, Vietnam, Netherlands, and Ireland (to name a few). In the United States, subsidence is currently being monitored by the United States Geological Survey (USGS). They have currently logged over 17,000 square miles of subsidence-affected areas across 45 states, 80% of which can be attributed to excessive ground water use. To specify an earlier statement, while subsidence cannot exactly be observed with the naked eye without prior knowledge, it can still be observed in its outward and direct affects. Evidently, lowering the ground is the effect, but of course there exist secondary effects from such dramatic geological changes. The effects of this change, referred to as cumulative compaction, can be divided into two sections: those on natural systems and those on manmade infrastructure. Effects on natural systems: As aforementioned and stressed, subsidence can damage natural water conveyance systems. By compacting the unconsolidated sediments within the aquifer, the hydraulic conductivity of the aquifer drops significantly as there is less room (if any) for the water to move. Not only does this inhibit the flow of groundwater, but it also reduces the hydraulic capacity of an aquifer. Above ground, there exist depressions in the soil and ground. Currently this has been attributed to flooding, especially in the Houston area of Texas, although it is somewhat more likely that excessive output of water and lack of public drainage systems precipitated flooding (*although, in my opinion and research it appears more likely that subsidence has actually helped to filter this water into the ground [not necessarily aquifers though…]*).
Effects on man-made systems: The shifts in ground level inevitably affect the buildings which lie on it, as it quite literally creates an inequality in the surface heights on which the buildings are built and tuned to. Thus, subsidence may cause cracks in buildings or infrastructure, or even collapse it depending on the positioning. It also disrupts pipelines, railways, roads, and ironically enough, wells.
Current Solutions and Technologies As of now, there remains no real “solution” or cure for subsidence, simply because one would literally have to lift up the ground and physically restructure the sediment so that it was permeable enough for increased groundwater flow; this would then have to be followed by the introduction of new groundwater to recharge the aquifer, but the rate of seepage would depend entirely on the size of sediments and hydraulic conductivity, depth of the water table, and degree of saturation. Assuming a typical water depth to water table of ~15 meters, depending on these factors, water seepage could take a matter of minutes to several months, even years (if the sediments are small enough). While artificial recharges do exist and are used, they would not necessarily prevent nor undo the effects of subsidence.
Because such an option is evidently unrealistic, the only true option has been to manage water systems. Currently, states have been trying to limit deep-well pumping in order to constrain subsidence and permit aquifers to recharge. The creation of shallower groundwater aquifers has also been considered but no considerable action has been taken. -Inspiration- In efforts to maintain the structure of manmade-infrastructure and buildings, a company known as BioCement artificially created a “living cement” that will adjust the structural foundations and supports of buildings in response to shifts in the structural integrity of the building. In this case, if the ground beneath the foundations begins to sink, the bio cement will begin to grow to fill the depression). The cement can also repair and patch up cracks or external damages precipitated by subsidence. BioCement functions by including bacteria which participate in MICP (Microbial Induced Calcite Precipitation). Summarily, these bacteria are included in the cement mixture and are treated with nutrients (proteins, sugars, and nitrogen) to grow the population and thereafter create carbonate ions by catalyzing the separation of urea. These carbonate ions are later provided with calcium ions, which bonds to form calcium carbonate. This precipitate forms around nucleation sites such as soil and cement particles. The end result would be solid filaments of calcium carbonate, also known as limestone. --------------------------------------------------------------------------------------------------------------------- Design Projection:Use of Genetically Modified Shewanella benthica in Bioremediation of Subsidence-Afflicted Aquifers through MICP
The design proposed hereafter seeks to utilize MICP to create limestone within aquifers to strengthen the structural integrity of aquifers and therefore restructure them to withstand excessive drainage. In addition, it will maintain the storage-capabilities and permeability of the aquifer sediments rather than simply fill in the aquifer with limestone and thus block groundwater flow.
Why MICP? MICP has been chosen for this process because the ultimate precipitate, when exposed to calcium ions, is calcium carbonate, also known as calcite, or limestone. Aquifers must be permeable and porous, and unconsolidated limestone sediments meets both of these requirements; in fact, carbonate/limestone aquifers are one of five identified United States aquifers. By taking advantage of bacterial excretions of carbonate ions, proper limestone can be introduced into aquifers without adverse effects. MICP Process The overall process of the bioremediation of aquifers is not something can be conducted solely by the bacteria and does demand some external action by those applying them. Because the bacteria will only function in the presence of urea, and in fact need urea and calcium ions to actually secrete calcium carbonate (CaCO3). Once the bacteria have been introduced into the system, they must be fed urea first, and then calcium ions later on for the following reactions to precipitate:
~~Keep in mind that because this will be happening in an aquifer there is no concern for additional water to be added~~
CO(NH2)2 + H2O ---> NH2COOH + NH3 NH2COOH + H2O ---> NH3 + H2CO3 Ammonium and carbonic acid form bicarbonate and 2 moles of ammonium and hydroxide ions in water (3 &4). 2NH3 + 2H2O <--->2NH+4 +2OH− (3) H2CO3 <---> HCO−3 + H+ (4) The production of hydroxide ions results in the increase of pH, which in turn can shift the bicarbonate equilibrium, resulting in the formation of carbonate ions (5) HCO−3 + H+ + 2NH+4 +2OH− <---> CO3−2 + 2NH+4 + 2H2O (5) The produced carbonate ions precipitate in the presence of calcium ions as calcium carbonate crystals (6). Ca+2 + CO3−2 <---> CaCO3 (6) The final precipitate will also include ammonium ions.
Chassis The chassis must fit two requirements to be used in this process: 1) it must be able to survive in high pressure, aquatic environment, and 2) it must be sensitive to pressure changes in such a way that the stimulation of pressure change thereafter affects a receptor in its membrane which can thus be tied to a transcription factor for urease (which it does not need to possess).
This being said, the prime option appears Shewanella benthica, a deep-sea, gram-negative bacterium which is both a piezophile and psychrophile; evidently, these characteristics allow it to not only survive in extreme conditions but more specifically those which apply to deep aquifer systems. It also responds to pressure elevations with an increased expression of respiration functions
Modification The pressure-regulating operon that has been identified within S. benthica is known as cydD-C with an open reading frame noted as ORF3. and under a promoter activated by receptors sensitive to pressure elevations, it begins to be expressed. In turn, it generally increases management of respiratory functions. Using this operon and its promoter, we are given the first necessary “key” or switch for MICP to begin.
The second essential part would have to be a transport protein that permits the entrance of urea into the cell for manufacturing and the initiation of Urease transcription. By utilizing a constitutive transport protein, and hence a protein that would always be “turned on”, or rather, always be transporting urea, the bacterial strain would fulfill two purposes: 1) limit the excess pollution of urea molecules and 2) maximize calcium carbonate output when necessary. The best possibility for this would be to isolate the transcription sequence that codes for the Yersinia Urea Transport protein within Yersinia pseudotuberculosis. The reason this transport protein was specifically chosen was because it always remains in the open state and is therefore constituent, hence suiting the required condition for the ideal bacterium projected by this project.
The final necessary component would be the transcriptional activator and transcription sequence which codes for the production of urease in response to urea particles. Proteus mirabilis contains the positive transcriptional activator known as UreR, which in the presence of urea activates the expression of UreD and UreA, the ure_ gene clusters responsible for the transcription of urease within its genome. These sequences can be inserted into the modified S. benthica’s genome around the cydD-C promoter, whereas the transcriptional activator would be inserted on the exterior of the promoter to direct tRNA only in response to the presence of urea, and the actual transcription sequences would be placed within ORF3 after the cydD-C.
Application The project would be applied in two steps. First, the modified S. benthica would be injected into a well. Keep in mind that the use of this bacteria is to heal the ground and therefore is for a targeted audience of those who either manage wells (such as individuals who run farms) or for use by (regional/state/national) government officials who must manage such geological changes. Through an injection well the bacteria should diffuse throughout the aquifer and settle within the sediments creating the aquifer. As the bacteria respond to increasing pressure from subsidence (which is a gradual and constant process) urea and calcium ions would be introduced as the second step and calcium carbonate would begin its precipitation.
Desired and Projected Result In projection, the bacteria should either settle amidst the aquifer’s sediment particles and wait for MICP to begin or they should be suspended in the water. After MICP, limestone should have done one of three things. The first possibility is that it cemented some loose sediments together, which would reinforce the sediments and therefore the aquifer to withstand subsidence. The second possibility is that it created unconsolidated limestone particles which would act as support particles that would allow the aquifer to remain permeable while still adding structural supports. The final possibility is that the bacteria precipitated limestone around current sediments, not necessarily cementing them together but rather coating them and giving them a stronger shell to withstand compression. In a macro sense, the precipitation of limestone should add structural supports to reinforce current sediments to withstand and therefore halt subsidence in the areas. An evident concern however is that the bacteria will cement the sediments together completely, thus preventing water from flowing through by consolidating the sediment. This can be controlled simply by letting the bacteria die due to lack of food/nutrition or even “suicide” in that they tend to coat themselves with limestone and therefore cut themselves off.
Increased Pressure
Urea
Urease
Calcium Carbonate
0
0
0
0
0
1
0
0
1
0
0
0
1
1
1
1
Pros and Cons Pros: The primary pro of this process are that these bacteria will be easy to grow cheaply and therefore easy to mass produce. At little to no labor we can begin to resist subsidence and halt the sinking of ground while also preventing millions of dollars being spent in efforts to repair natural land and manmade structures harmed by subsidence. In addition, it can rather easily be introduced into well and aquifer systems, while also precipitating limestone, which is naturally used in aquifers and therefore is already observed as a successful material for hydraulic conduction.
Cons: The primary con of this process is that one of the products is ammonium ions which can be harmful to humans. Because this process deals solely with groundwater, and hence our drinking water, filtration or distillation or some process of purification while the process is in place.
Testing Testing would first involve invoking increases in pressure to make sure that increased pressure would activate the necessary genes. Testing would also include injecting the genetically modified S. benthica into a model high-pressure system of unconsolidated sediments in an aquatic environment and measuring the rate of CaCO3 production as well as bacterial growth to accurately measure the total precipitation and therefore avoid (during actual application) complete cementation. Another factor that should be tested is bacterial life length without nutrients. Sources
Anbu, Periasamy, Chang-Ho Kang, Yu-Jin Shin, and Jae-Seong So. "Formations of Calcium Carbonate Minerals By Bacteria and its Multiple Applications." National Center for Biotechnology Information. Springer International Publishing, 2016. Web. 13 July 2017.
Dattelbaum, J. D., C. V. Lockatell, D. E. Johnson, and H. L. Mobley. "UreR, the Transcriptional Activator of the Proteus mirabilis Urease Gene Cluster, is Required for Urease Activity and Virulence in Experimental Urinary Tract Infections." National Center for Biotechnology Information. U.S. National Library of Medicine, Feb. 2003. Web. 13 July 2017.
USGS. "Land Subsidence: Cause & Effect." USGS Water Science Center. N.p., n.d. Web. 13 July 2017.
Larsson, Magnus. "Turning Dunes into Architecture." TED. N.p., n.d. Web. 13 July 2017.
Lauro, F. M., R. A. Chastain, S. Ferriera, J. Johnson, A. A. Yayanos, and D. H. Bartlett. "Draft Genome Sequence of the Deep-Sea Bacterium Shewanella benthica Strain KT99." National Center for Biotechnology Information. American Society for Microbiology, 2013. Web. 13 July 2017.
Matchar, Emily. "With This Self-Healing Concrete, Buildings Repair Themselves." Smithsonian. Smithsonian Institution, 05 June 2015. Web. 13 July 2017.
Mobley, Harry L. T. Helicobacter pylori: Physiology and Genetics. Washington: American Society for Microbiology, 2001. National Center for Biotechnology Information. Web.
Pflock, Michael, Simone Kennard, Isabel Delany, Vincenzo Scarlato, and Dagmar Beier. "Acid-Induced Activation of the Urease Promoters Is Mediated Directly by the ArsRS Two-Component System of Helicobacter pylori." National Center for Biotechnology Information. American Society for Microbiology, Oct. 2005. Web. 13 July 2017.
USGS. USGS: Land Subsidence in the United States. N.p.: n.p., n.d. Print.
As far as science goes, I'm kind of all over the place. I've studied and researched subjects all the way from hydrogeology to alternate energy to biodiversity/conservation genetics. The common factor here has been a strong interest in environmental sciences and the application of such for a cleaner and more earth-friendly future.
I look forward to getting to know you all!
Design Presentation: Bioremediation of Subsidence through Microbial Induced Calcite Precipitation
What is Subsidence?
Simply defined, land subsidence is the lowering of the ground level. To clarify, subsidence does not involve sinkholes, which occur due to the dissolution of soluble bedrock by water in a respectively small area. Rather, subsidence is a result of a lack of water within an aquifer that generally affects a large area, and therefore is often unable to be observed without prior cognition of the issue or access to machines called extensometers.
By natural processes, this can be the outcome of tectonic activities or the compression of land and withdrawal of water by the generation of ice sheets over the Earth’s crust. While the natural procession of subsidence does present a threat to current land possessions and man-made establishments, the true concern is artificially-induced subsidence precipitated from human activities. Human-induced land subsidence has not only catalyzed natural subsidence but has rapidly stimulated lowering in areas otherwise indisposed to such dramatic geologic change. Primarily, land subsidence is induced by oil and gas drilling which interferes with an aquifer’s structural integrity, and more significantly, the excessive drainage of water from aquifer’s. This last method which quite literally drains it of essential support.
Drainage-induced subsidence can ultimately be illustrated as the following. Recall the water table— the area beneath the earth in which lies [water] saturated bedrock. This saturated bedrock is called an aquifer, through which ground water filters and flows. The groundwater within non-polluted aquifers is not only essential for fulfilling nutritional requirements, but also for irrigation, farming, and manufacturing processes, and therefore aquifers are tapped into through wells and the likes. However, the overexertion of these wells and strained drainage in order to fulfill these needs often results in an insufficient quantity of water remaining in the aquifer; not only that, but it also undermines its ability to recuperate the water it has lost.
Because the water within aquifers is actually essential to holding up the ground, by withdrawing it without permitting it to sufficiently recover, the ground literally “caves” in on itself. The bedrock particles compact together, closing drainage and underground water systems and therefore prohibiting flow as well as restricting storage capacity. This is the most prominent form of subsidence, and currently it presents a strong yet often-overlooked and unidentified danger to our world.
Observable Effects
--From here on, when I refer to subsidence I will be referring to human-induced subsidence, primarily as a result of excessive aquifer-drainage--
Subsidence is still a developing issue, as the public lacks much awareness of its existence, processes, effects, and hazard. That being said, it is a persistent and unavoidable occurrence that will persevere as long as our current needs and methodology do not consider the effects they precipitate. Presently, subsidence is rampant not only in the United States, but also Thailand, Japan, Italy, Vietnam, Netherlands, and Ireland (to name a few).
In the United States, subsidence is currently being monitored by the United States Geological Survey (USGS). They have currently logged over 17,000 square miles of subsidence-affected areas across 45 states, 80% of which can be attributed to excessive ground water use.
To specify an earlier statement, while subsidence cannot exactly be observed with the naked eye without prior knowledge, it can still be observed in its outward and direct affects. Evidently, lowering the ground is the effect, but of course there exist secondary effects from such dramatic geological changes. The effects of this change, referred to as cumulative compaction, can be divided into two sections: those on natural systems and those on manmade infrastructure.
Effects on natural systems: As aforementioned and stressed, subsidence can damage natural water conveyance systems. By compacting the unconsolidated sediments within the aquifer, the hydraulic conductivity of the aquifer drops significantly as there is less room (if any) for the water to move. Not only does this inhibit the flow of groundwater, but it also reduces the hydraulic capacity of an aquifer. Above ground, there exist depressions in the soil and ground. Currently this has been attributed to flooding, especially in the Houston area of Texas, although it is somewhat more likely that excessive output of water and lack of public drainage systems precipitated flooding (*although, in my opinion and research it appears more likely that subsidence has actually helped to filter this water into the ground [not necessarily aquifers though…]*).
Effects on man-made systems: The shifts in ground level inevitably affect the buildings which lie on it, as it quite literally creates an inequality in the surface heights on which the buildings are built and tuned to. Thus, subsidence may cause cracks in buildings or infrastructure, or even collapse it depending on the positioning. It also disrupts pipelines, railways, roads, and ironically enough, wells.
Current Solutions and Technologies
As of now, there remains no real “solution” or cure for subsidence, simply because one would literally have to lift up the ground and physically restructure the sediment so that it was permeable enough for increased groundwater flow; this would then have to be followed by the introduction of new groundwater to recharge the aquifer, but the rate of seepage would depend entirely on the size of sediments and hydraulic conductivity, depth of the water table, and degree of saturation. Assuming a typical water depth to water table of ~15 meters, depending on these factors, water seepage could take a matter of minutes to several months, even years (if the sediments are small enough). While artificial recharges do exist and are used, they would not necessarily prevent nor undo the effects of subsidence.
Because such an option is evidently unrealistic, the only true option has been to manage water systems. Currently, states have been trying to limit deep-well pumping in order to constrain subsidence and permit aquifers to recharge. The creation of shallower groundwater aquifers has also been considered but no considerable action has been taken.
-Inspiration-
In efforts to maintain the structure of manmade-infrastructure and buildings, a company known as BioCement artificially created a “living cement” that will adjust the structural foundations and supports of buildings in response to shifts in the structural integrity of the building. In this case, if the ground beneath the foundations begins to sink, the bio cement will begin to grow to fill the depression). The cement can also repair and patch up cracks or external damages precipitated by subsidence.
BioCement functions by including bacteria which participate in MICP (Microbial Induced Calcite Precipitation). Summarily, these bacteria are included in the cement mixture and are treated with nutrients (proteins, sugars, and nitrogen) to grow the population and thereafter create carbonate ions by catalyzing the separation of urea. These carbonate ions are later provided with calcium ions, which bonds to form calcium carbonate. This precipitate forms around nucleation sites such as soil and cement particles. The end result would be solid filaments of calcium carbonate, also known as limestone.
---------------------------------------------------------------------------------------------------------------------
Design Projection:Use of Genetically Modified Shewanella benthica in Bioremediation of Subsidence-Afflicted Aquifers through MICP
The design proposed hereafter seeks to utilize MICP to create limestone within aquifers to strengthen the structural integrity of aquifers and therefore restructure them to withstand excessive drainage. In addition, it will maintain the storage-capabilities and permeability of the aquifer sediments rather than simply fill in the aquifer with limestone and thus block groundwater flow.
Why MICP?
MICP has been chosen for this process because the ultimate precipitate, when exposed to calcium ions, is calcium carbonate, also known as calcite, or limestone. Aquifers must be permeable and porous, and unconsolidated limestone sediments meets both of these requirements; in fact, carbonate/limestone aquifers are one of five identified United States aquifers. By taking advantage of bacterial excretions of carbonate ions, proper limestone can be introduced into aquifers without adverse effects.
MICP Process
The overall process of the bioremediation of aquifers is not something can be conducted solely by the bacteria and does demand some external action by those applying them. Because the bacteria will only function in the presence of urea, and in fact need urea and calcium ions to actually secrete calcium carbonate (CaCO3).
Once the bacteria have been introduced into the system, they must be fed urea first, and then calcium ions later on for the following reactions to precipitate:
~~Keep in mind that because this will be happening in an aquifer there is no concern for additional water to be added~~
CO(NH2)2 + H2O ---> NH2COOH + NH3
NH2COOH + H2O ---> NH3 + H2CO3
Ammonium and carbonic acid form bicarbonate and 2 moles of ammonium and hydroxide ions in water (3 &4).
2NH3 + 2H2O <--->2NH+4 +2OH− (3) H2CO3 <---> HCO−3 + H+ (4)
The production of hydroxide ions results in the increase of pH, which in turn can shift the bicarbonate equilibrium, resulting in the formation of carbonate ions (5)
HCO−3 + H+ + 2NH+4 +2OH− <---> CO3−2 + 2NH+4 + 2H2O (5)
The produced carbonate ions precipitate in the presence of calcium ions as calcium carbonate crystals (6).
Ca+2 + CO3−2 <---> CaCO3 (6)
The final precipitate will also include ammonium ions.
Chassis
The chassis must fit two requirements to be used in this process: 1) it must be able to survive in high pressure, aquatic environment, and 2) it must be sensitive to pressure changes in such a way that the stimulation of pressure change thereafter affects a receptor in its membrane which can thus be tied to a transcription factor for urease (which it does not need to possess).
This being said, the prime option appears Shewanella benthica, a deep-sea, gram-negative bacterium which is both a piezophile and psychrophile; evidently, these characteristics allow it to not only survive in extreme conditions but more specifically those which apply to deep aquifer systems. It also responds to pressure elevations with an increased expression of respiration functions
Modification
The pressure-regulating operon that has been identified within S. benthica is known as cydD-C with an open reading frame noted as ORF3. and under a promoter activated by receptors sensitive to pressure elevations, it begins to be expressed. In turn, it generally increases management of respiratory functions. Using this operon and its promoter, we are given the first necessary “key” or switch for MICP to begin.
The second essential part would have to be a transport protein that permits the entrance of urea into the cell for manufacturing and the initiation of Urease transcription. By utilizing a constitutive transport protein, and hence a protein that would always be “turned on”, or rather, always be transporting urea, the bacterial strain would fulfill two purposes: 1) limit the excess pollution of urea molecules and 2) maximize calcium carbonate output when necessary. The best possibility for this would be to isolate the transcription sequence that codes for the Yersinia Urea Transport protein within Yersinia pseudotuberculosis. The reason this transport protein was specifically chosen was because it always remains in the open state and is therefore constituent, hence suiting the required condition for the ideal bacterium projected by this project.
The final necessary component would be the transcriptional activator and transcription sequence which codes for the production of urease in response to urea particles. Proteus mirabilis contains the positive transcriptional activator known as UreR, which in the presence of urea activates the expression of UreD and UreA, the ure_ gene clusters responsible for the transcription of urease within its genome. These sequences can be inserted into the modified S. benthica’s genome around the cydD-C promoter, whereas the transcriptional activator would be inserted on the exterior of the promoter to direct tRNA only in response to the presence of urea, and the actual transcription sequences would be placed within ORF3 after the cydD-C.
Application
The project would be applied in two steps. First, the modified S. benthica would be injected into a well. Keep in mind that the use of this bacteria is to heal the ground and therefore is for a targeted audience of those who either manage wells (such as individuals who run farms) or for use by (regional/state/national) government officials who must manage such geological changes. Through an injection well the bacteria should diffuse throughout the aquifer and settle within the sediments creating the aquifer. As the bacteria respond to increasing pressure from subsidence (which is a gradual and constant process) urea and calcium ions would be introduced as the second step and calcium carbonate would begin its precipitation.
Desired and Projected Result
In projection, the bacteria should either settle amidst the aquifer’s sediment particles and wait for MICP to begin or they should be suspended in the water. After MICP, limestone should have done one of three things. The first possibility is that it cemented some loose sediments together, which would reinforce the sediments and therefore the aquifer to withstand subsidence. The second possibility is that it created unconsolidated limestone particles which would act as support particles that would allow the aquifer to remain permeable while still adding structural supports. The final possibility is that the bacteria precipitated limestone around current sediments, not necessarily cementing them together but rather coating them and giving them a stronger shell to withstand compression.
In a macro sense, the precipitation of limestone should add structural supports to reinforce current sediments to withstand and therefore halt subsidence in the areas.
An evident concern however is that the bacteria will cement the sediments together completely, thus preventing water from flowing through by consolidating the sediment. This can be controlled simply by letting the bacteria die due to lack of food/nutrition or even “suicide” in that they tend to coat themselves with limestone and therefore cut themselves off.
Pros and Cons
Pros: The primary pro of this process are that these bacteria will be easy to grow cheaply and therefore easy to mass produce. At little to no labor we can begin to resist subsidence and halt the sinking of ground while also preventing millions of dollars being spent in efforts to repair natural land and manmade structures harmed by subsidence. In addition, it can rather easily be introduced into well and aquifer systems, while also precipitating limestone, which is naturally used in aquifers and therefore is already observed as a successful material for hydraulic conduction.
Cons: The primary con of this process is that one of the products is ammonium ions which can be harmful to humans. Because this process deals solely with groundwater, and hence our drinking water, filtration or distillation or some process of purification while the process is in place.
Testing
Testing would first involve invoking increases in pressure to make sure that increased pressure would activate the necessary genes. Testing would also include injecting the genetically modified S. benthica into a model high-pressure system of unconsolidated sediments in an aquatic environment and measuring the rate of CaCO3 production as well as bacterial growth to accurately measure the total precipitation and therefore avoid (during actual application) complete cementation. Another factor that should be tested is bacterial life length without nutrients.
Sources
Anbu, Periasamy, Chang-Ho Kang, Yu-Jin Shin, and Jae-Seong So. "Formations of Calcium Carbonate Minerals By Bacteria and its Multiple Applications." National Center for Biotechnology Information. Springer International Publishing, 2016. Web. 13 July 2017.
Dattelbaum, J. D., C. V. Lockatell, D. E. Johnson, and H. L. Mobley. "UreR, the Transcriptional Activator of the Proteus mirabilis Urease Gene Cluster, is Required for Urease Activity and Virulence in Experimental Urinary Tract Infections." National Center for Biotechnology Information. U.S. National Library of Medicine, Feb. 2003. Web. 13 July 2017.
EMBL-EBI, InterPro. "Urea Transporter: Bacteria (IPR017807)." InterPro. N.p., n.d. Web. 13 July 2017.
Kato, Chiaki. Pressure Response in Deep-Sea Piezophilic Bacteria. JMMB, n.d. Web.
USGS. "Land Subsidence: Cause & Effect." USGS Water Science Center. N.p., n.d. Web. 13 July 2017.
Larsson, Magnus. "Turning Dunes into Architecture." TED. N.p., n.d. Web. 13 July 2017.
Lauro, F. M., R. A. Chastain, S. Ferriera, J. Johnson, A. A. Yayanos, and D. H. Bartlett. "Draft Genome Sequence of the Deep-Sea Bacterium Shewanella benthica Strain KT99." National Center for Biotechnology Information. American Society for Microbiology, 2013. Web. 13 July 2017.
Matchar, Emily. "With This Self-Healing Concrete, Buildings Repair Themselves." Smithsonian. Smithsonian Institution, 05 June 2015. Web. 13 July 2017.
Mobley, Harry L. T. Helicobacter pylori: Physiology and Genetics. Washington: American Society for Microbiology, 2001. National Center for Biotechnology Information. Web.
Pflock, Michael, Simone Kennard, Isabel Delany, Vincenzo Scarlato, and Dagmar Beier. "Acid-Induced Activation of the Urease Promoters Is Mediated Directly by the ArsRS Two-Component System of Helicobacter pylori." National Center for Biotechnology Information. American Society for Microbiology, Oct. 2005. Web. 13 July 2017.
USGS. USGS: Land Subsidence in the United States. N.p.: n.p., n.d. Print.